How I Helped My Junior Developer Fix 934 Git Unstaged Changes (And You Can Too!)

Last week, I received a panicked message from a junior , Lets call her Siya for this blog. She wrote : "I have 934 unstaged changes in my Git repo and VS Code is going crazy! What do I do?"

Sound familiar? This is one of the most common Git disasters junior developers face, and the solution isn't always obvious. Here's how we fixed it together, step by step.

The Problem: When Git Goes Wild

Siya opened her terminal and ran git status, only to see something like this:

On branch master
No commits yet
Untracked files:
  .cache/
  .conda/
  .cursor/
  AppData/
  Contacts/
  Documents/
  Downloads/
  Music/
  Videos/
  project1/
  project2/
  project3/
  # ... and 900+ more files

Plus those dreaded permission warnings:

warning: could not open directory 'AppData/Local/Application Data/': Permission denied
warning: could not open directory 'Documents/My Music/': Permission denied

The Root Cause: She had accidentally initialized a Git repository in her Windows user directory (C:\Users\MainDirectory\) instead of in a specific project folder. Git was trying to track her entire user profile - system files, personal documents, application data, and all her projects mixed together!

Step 1: Emergency Stop - Remove the Problematic Repository

First things first - we needed to remove the Git repository from her user directory:

# Navigate to user directory
cd C:\Users\MainDirectory

# Remove the .git folder (this deletes the repository)
Remove-Item -Force -Recurse .git

# Verify it's gone
git status
# Should show: "fatal: not a git repository"

✅ Crisis averted! No more 934 unstaged changes.

Step 2: Organize the Chaos

Siya's user directory was a mess - project folders mixed with system directories. We organized it properly:

# Create a dedicated Projects folder
mkdir Projects

# Move all actual projects into it
Move-Item project1, project2, project3, project4, project5, project6, project7 Projects\

Now her user directory was clean, with only:

• System folders (Documents, Downloads, etc.)

• Configuration files (.gitconfig, etc.)

• Her organized Projects folder

Step 3: The Python Project Surprise

When we tried to set up Git for her project1 (a Python web application), we discovered it already had a repository, but with a different problem:

cd Projects\project1
git status

This showed hundreds of Python cache files being tracked:

modified:   project1/Lib/site-packages/__pycache__/google_auth_httplib2.cpython-311.pyc
modified:   project1/Lib/site-packages/__pycache__/typing_extensions.cpython-311.pyc
# ... hundreds more .pyc files

The Issue: The .gitignore file had been deleted, so Git started tracking Python's automatically generated cache files.

Step 4: The Python Project Fix

We created a proper .gitignore file for Python projects:

# Create a comprehensive Python .gitignore
# Note: This is for python project. Select the template relevent to your project.
@"
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# Virtual environment
Lib/
Scripts/
Include/
pyvenv.cfg

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg

# Environment variables
.env
.venv

# IDE
.vscode/
.idea/

# OS
.DS_Store
Thumbs.db
"@ | Out-File -FilePath .gitignore -Encoding utf8

Magic moment: The unstaged changes dropped from 934+ to just 7 legitimate files!

Step 5: Clean Up and Commit

Finally, we staged the real changes and cleaned up:

# Navigate to the actual source code directory
cd project1

# Add legitimate changes
git add file1.py file2.py file3.py file4.py Procfile

# Remove deleted files from tracking
git rm old_file.py .gitignore tempfile
# Go back to project root and add the new .gitignore
cd ..
git add .gitignore

# Commit everything
git commit -m "Add proper .gitignore and clean up project files"

# Check the result
git status
# "nothing to commit, working tree clean" ✅

Key Lessons for Beginners

1. Always Check Your Location Before git init

pwd  # or 'cd' on Windows - know where you are!

2. Use Proper .gitignore Files

For Python projects, never commit:

• __pycache__/ folders

• .pyc files

• Virtual environment folders (Lib/, Scripts/, Include/)

• .env files with secrets

3. Organize Your Projects

Don't mix projects with system files. Use a structure like:

C:\Users\MainDirectory\
├── Documents\
├── Downloads\
└── Projects\
    ├── project1\
    ├── project2\
    └── project3\

4. When Things Go Wrong

• Don't panic

• Remove the problematic .git folder if needed

• Start fresh with proper organization

• Use appropriate .gitignore files

Prevention is Better Than Cure

Before starting any new project:

1. Create a dedicated project directory

2. Navigate into it: cd your-project

3. Initialize Git: git init

4. Create .gitignore first: touch .gitignore (or copy from templates)

5. Then start coding

Tools That Help

• GitHub's .gitignore templates: https://github.com/github/gitignore

• gitignore.io: Generate .gitignore files for any tech stack

• VS Code Extensions: GitLens, Git Graph for better Git visualization

The Happy Ending

After our cleanup session, Siya's development environment was pristine:

• Clean, organized project structure

• Proper Git repositories for each project

• No more system files in version control

• A much happier VS Code experience

She thanked me and said, "I wish I knew this when I started coding!"

That's exactly why I am sharing this story. Every developer faces these issues, but with the right approach, they're totally fixable.

Your Turn

Have you faced similar Git disasters? Share your stories in the comments! And remember - we've all been there. The important thing is learning from these experiences and helping the next developer who runs into the same problem.

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Remember: Git is powerful, but with great power comes great responsibility. Always know where you are and what you're tracking!